Nature Microbiology最新文献

{"title":"Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis","authors":"Ting Zhang, Yuko Hasegawa, Matthew K. Waldor","doi":"10.1038/s41564-024-01862-z","DOIUrl":"10.1038/s41564-024-01862-z","url":null,"abstract":"The liver makes bile, an aqueous solution critical for fat absorption, which is secreted into the duodenum. Despite extensive studies on bile salts, other components of bile are less well characterized. Here we used global metabolomic analysis on bile from specific-pathogen-free, germ-free, Citrobacter rodentium-infected or Listeria monocytogenes-infected mice and identified a metabolome of 812 metabolites that were altered by both microbiota and enteric infection. Hepatic transcriptomics identified enteric-infection-triggered pathways that probably underlie bile remodelling. Enteric infection increased levels of four dicarboxylates in bile, including itaconate. Analysis of Acod1−/− mice indicated that increased itaconate also increased tuft cell abundance, altered microbiota composition and function as detected by metagenomic analysis, and modulated host defence, leading to reduced Vibrio cholerae colonization. Our data suggest that enteric-infection-associated signals are relayed between the intestine and liver and induce transcriptional programmes that shape the bile metabolome, modifying the immunomodulatory and host defence functions of bile. Metabolomic analysis of bile after infection by enteric bacteria in mice reveals composition changes including increased itaconate levels that promote intestinal homeostasis and reduce Vibrio cholerae colonization.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3376-3390"},"PeriodicalIF":20.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01862-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Searching for high pathogenicity avian influenza virus in Antarctica","authors":"Begoña Aguado, Lineke Begeman, Anne Günther, Matteo Iervolino, Florencia Soto, Ralph E. T. Vanstreels, Alice Reade, Adam Coerper, Ben Wallis, Antonio Alcamí, Meagan Dewar","doi":"10.1038/s41564-024-01868-7","DOIUrl":"10.1038/s41564-024-01868-7","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3081-3083"},"PeriodicalIF":20.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial chemotaxis toward virus-infected cyanobacteria","authors":"Uri Sheyn, Maria P. Erazo-Garcia, Frank O. Aylward","doi":"10.1038/s41564-024-01867-8","DOIUrl":"10.1038/s41564-024-01867-8","url":null,"abstract":"During the pre-lysis phases of phage infection, the cyanobacterium Synechococcus releases metabolites that attract heterotrophic bacteria — a process that is likely to influence carbon fate in the ocean.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3093-3094"},"PeriodicalIF":20.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts","authors":"Paolo Manghi, Amrisha Bhosle, Kai Wang, Roberta Marconi, Marta Selma-Royo, Liviana Ricci, Francesco Asnicar, Davide Golzato, Wenjie Ma, Dong Hang, Kelsey N. Thompson, Eric A. Franzosa, Amir Nabinejad, Sabrina Tamburini, Eric B. Rimm, Wendy S. Garrett, Qi Sun, Andrew T. Chan, Mireia Valles-Colomer, Manimozhiyan Arumugam, Kate M. Bermingham, Francesca Giordano, Richard Davies, George Hadjigeorgiou, Jonathan Wolf, Till Strowig, Sarah E. Berry, Curtis Huttenhower, Tim D. Spector, Nicola Segata, Mingyang Song","doi":"10.1038/s41564-024-01858-9","DOIUrl":"10.1038/s41564-024-01858-9","url":null,"abstract":"Although diet is a substantial determinant of the human gut microbiome, the interplay between specific foods and microbial community structure remains poorly understood. Coffee is a habitually consumed beverage with established metabolic and health benefits. We previously found that coffee is, among >150 items, the food showing the highest correlation with microbiome components. Here we conducted a multi-cohort, multi-omic analysis of US and UK populations with detailed dietary information from a total of 22,867 participants, which we then integrated with public data from 211 cohorts (N = 54,198). The link between coffee consumption and microbiome was highly reproducible across different populations (area under the curve of 0.89), largely driven by the presence and abundance of the species Lawsonibacter asaccharolyticus. Using in vitro experiments, we show that coffee can stimulate growth of L. asaccharolyticus. Plasma metabolomics on 438 samples identified several metabolites enriched among coffee consumers, with quinic acid and its potential derivatives associated with coffee and L. asaccharolyticus. This study reveals a metabolic link between a specific gut microorganism and a specific food item, providing a framework for the understanding of microbial dietary responses at the biochemical level. Coffee consumption is associated with the presence and abundance of a specific member of the human gut microbiome, Lawsonibacter asaccharolyticus, and changes to the plasma metabolome.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3120-3134"},"PeriodicalIF":20.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01858-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary zinc deficiency promotes Acinetobacter baumannii lung infection via IL-13 in mice","authors":"Lauren D. Palmer, Kacie A. Traina, Lillian J. Juttukonda, Zachery R. Lonergan, Dziedzom A. Bansah, Xiaomei Ren, John H. Geary, Christopher Pinelli, Kelli L. Boyd, Tzushan S. Yang, Eric P. Skaar","doi":"10.1038/s41564-024-01849-w","DOIUrl":"10.1038/s41564-024-01849-w","url":null,"abstract":"Dietary zinc deficiency is a major risk factor for pneumonia. Acinetobacter baumannii is a leading cause of ventilator-associated pneumonia and a critical public health threat due to increasing rates of multidrug resistance. Patient populations at increased risk for A. baumannii pneumonia are also at increased risk of zinc deficiency. Here we established a mouse model of dietary zinc deficiency and acute A. baumannii pneumonia to test the hypothesis that host zinc deficiency contributes to A. baumannii pathogenesis. We showed that zinc-deficient mice have significantly increased A. baumannii burdens in the lungs, dissemination to the spleen and higher mortality. During infection, zinc-deficient mice produce more pro-inflammatory cytokines, including IL-13. Administration of IL-13 promotes A. baumannii dissemination in zinc-sufficient mice, while antibody neutralization of IL-13 protects zinc-deficient mice from A. baumannii dissemination and mortality during infection. These data highlight the therapeutic potential of anti-IL-13 antibody treatments, which are well tolerated in humans, for the treatment of pneumonia. Increased IL-13 drives increased bacterial dissemination and mortality following Acinetobacter baumannii lung infection of zinc-deficient mice and can be countered by anti-IL-13 antibody therapy.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3196-3209"},"PeriodicalIF":20.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria","authors":"Richard J. Henshaw, Jonathan Moon, Michael R. Stehnach, Benjamin P. Bowen, Suzanne M. Kosina, Trent R. Northen, Jeffrey S. Guasto, Sheri A. Floge","doi":"10.1038/s41564-024-01843-2","DOIUrl":"10.1038/s41564-024-01843-2","url":null,"abstract":"Chemical cues mediate interactions between marine phytoplankton and bacteria, underpinning ecosystem-scale processes including nutrient cycling and carbon fixation. Phage infection alters host metabolism, stimulating the release of chemical cues from intact plankton, but how these dynamics impact ecology and biogeochemistry is poorly understood. Here we determine the impact of phage infection on dissolved metabolite pools from marine cyanobacteria and the subsequent chemotactic response of heterotrophic bacteria using time-resolved metabolomics and microfluidics. Metabolites released from intact, phage-infected Synechococcus elicited strong chemoattraction from Vibrio alginolyticus and Pseudoalteromonas haloplanktis, especially during early infection stages. Sustained bacterial chemotaxis occurred towards live-infected Synechococcus, contrasted by no discernible chemotaxis towards uninfected cyanobacteria. High-throughput microfluidics identified 5′-deoxyadenosine and 5′-methylthioadenosine as key attractants. Our findings establish that, before lysis, phage-infected picophytoplankton release compounds that attract motile heterotrophic bacteria, suggesting a mechanism for resource transfer that might impact carbon and nutrient fluxes across trophic levels. The authors use time-resolved metabolomics and microfluidics to characterize enhanced heterotroph chemoattraction to metabolites released from cyanobacteria during early stages of phage infection.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3184-3195"},"PeriodicalIF":20.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell imaging of the Mycobacterium tuberculosis cell cycle reveals linear and heterogenous growth","authors":"Eun Seon Chung, Prathitha Kar, Maliwan Kamkaew, Ariel Amir, Bree B. Aldridge","doi":"10.1038/s41564-024-01846-z","DOIUrl":"10.1038/s41564-024-01846-z","url":null,"abstract":"Difficulties in antibiotic treatment of Mycobacterium tuberculosis (Mtb) are partly thought to be due to heterogeneity in growth. Although the ability of bacterial pathogens to regulate growth is crucial to control homeostasis, virulence and drug responses, single-cell growth and cell cycle behaviours of Mtb are poorly characterized. Here we use time-lapse, single-cell imaging of Mtb coupled with mathematical modelling to observe asymmetric growth and heterogeneity in cell size, interdivision time and elongation speed. We find that, contrary to Mycobacterium smegmatis, Mtb initiates cell growth not only from the old pole but also from new poles or both poles. Whereas most organisms grow exponentially at the single-cell level, Mtb has a linear growth mode. Our data show that the growth behaviour of Mtb diverges from that of model bacteria, provide details into how Mtb grows and creates heterogeneity and suggest that growth regulation may also diverge from that in other bacteria. Time-lapse imaging of Mycobacterium tuberculosis cells loaded in microfluidic chambers reveals heterogeneity in growth characteristics, atypical modes of polar growth initiation and linear growth at the single-cell level.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3332-3344"},"PeriodicalIF":20.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01846-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimates of microbiome heritability across hosts","authors":"Andrew H. Morris, Brendan J. M. Bohannan","doi":"10.1038/s41564-024-01865-w","DOIUrl":"10.1038/s41564-024-01865-w","url":null,"abstract":"Microbiomes contribute to variation in many plant and animal traits, suggesting that microbiome-mediated traits could evolve through selection on the host. However, for such evolution to occur, microbiomes must exhibit sufficient heritability to contribute to host adaptation. Previous work has attempted to estimate the heritability of a variety of microbiome attributes. Here we show that most published estimates are limited to vertebrate and plant hosts, but significant heritability of microbiome attributes has been frequently reported. This indicates that microbiomes could evolve in response to host-level selection, but studies across a wider range of hosts are necessary before general conclusions can be made. We suggest future studies focus on standardizing heritability measurements for the purpose of meta-analyses and investigate the role of the environment in contributing to heritable microbiome variation. This could have important implications for the use of microbiomes in conservation, agriculture and medicine. In this Perspective, Morris and Bohannan discuss heritability of microbiome-mediated traits across hosts and future research questions with implications for animal and plant breeding.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3110-3119"},"PeriodicalIF":20.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A method to detect origin of transfer sequences for plasmid conjugation","authors":"","doi":"10.1038/s41564-024-01845-0","DOIUrl":"10.1038/s41564-024-01845-0","url":null,"abstract":"Plasmid conjugation has been extensively studied over the past decades. Yet, in most plasmids, the minimal region required for conjugation (the origin of transfer (oriT) sequence) is unknown. The characterization of known oriTs enabled the development of a validated method to identify genomic regions with novel families of oriTs across bacterial plasmids.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3095-3096"},"PeriodicalIF":20.5,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial solutions must be deployed against climate catastrophe","authors":"Raquel Peixoto, Christian R. Voolstra, Lisa Y. Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A. Amin, Max Häggblom, Ann Gregory, Thulani P. Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T. Lennon, Antonio Ventosa, Patrik M. Bavoil, Virginia Miller, Jack A. Gilbert","doi":"10.1038/s41564-024-01861-0","DOIUrl":"10.1038/s41564-024-01861-0","url":null,"abstract":"This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 12","pages":"3084-3085"},"PeriodicalIF":20.5,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01861-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142599126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}